[gmx-users] The sum of the two largest charge group radii is larger than rlist

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 7 12:48:57 CEST 2014


On Mon, Apr 7, 2014 at 11:48 AM, pratibha <kapoorpratibha7 at gmail.com> wrote:

> Hi all
>
> I would like to first quench my system from 500K to 300K and then do NPT
> eqilibration followed by NPT production run. But while running grompp for
> NPT eqilibration, I am getting following error :
>
>   The sum of the two largest charge group radii (10.876598) is larger than
> rlist (1.000000)
>

This is probably caused by using the confout.gro from annealing, which
might have some molecule split over PBC if your box has some dimension
around 11nm. You can check that with your favourite visualization program.
Use trjconv to make molecules whole, and grompp will be happy.

Mark


>
>  My system contains protein, cosolvent and water molecules. I think my mdp
> settings are incompatible with the algorithm.
> I am using following parameters for quenching :
>
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 100000        ; 0.002 * 100000 = 200 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> cutoff-scheme   = Verlet
> nstxout         = 1000          ; save coordinates every 2 ps
> nstvout         = 1000          ; save velocities every 2 ps
> nstxtcout       = 1000          ; xtc compressed trajectory output every 2
> ps
> nstenergy       = 1000          ; save energies every 2 ps
> nstlog          = 1000          ; update log file every 2 ps
> ; Bond parameters
> ;continuation   = yes           ; Restarting after NPT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; two coupling groups - more
> accurate
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 300   300     ; reference temperature, one for each
> group,
> in K
> ; Pressure coupling is on
> pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
> pcoupltype      = isotropic     ; uniform scaling of box vectors
> tau_p           = 2.0           ; time constant, in ps
> ref_p           = 1.0           ; reference pressure, in bar
> compressibility = 4.5e-5        ; isothermal compressibility of water,
> bar^-1
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no            ; Velocity generation is off
> ; Quenching
> annealing = single single
> annealing_npoints = 21 21
> annealing_time = 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
> 170 180 190 200 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
> 170
> 180 190 200
> annealing_temp = 500 490 480 470 460 450 440 430 420 410 400 390 380 370
> 360
> 350 340 330 320 310 300 500 490 480 470 460 450 440 430 420 410 400 390 380
> 370 360 350 340 330 320 310 300
>
> And for NPT equilibration I am using :
>
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 50000         ; 2 * 50000 = 100 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 100           ; save coordinates every 0.2 ps
> nstvout         = 100           ; save velocities every 0.2 ps
> nstenergy       = 100           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = yes           ; Restarting after NVT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; two coupling groups - more
> accurate
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 300   300     ; reference temperature, one for each
> group,
> in K
> ; Pressure coupling is on
> pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
> pcoupltype      = isotropic     ; uniform scaling of box vectors
> tau_p           = 2.0           ; time constant, in ps
> ref_p           = 1.0           ; reference pressure, in bar
> compressibility = 4.5e-5        ; isothermal compressibility of water,
> bar^-1
> refcoord_scaling = com
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no            ; Velocity generation is off
>
> Please help me correct my mdp files (if required) so that I can accomplish
> my task.
> Thanks in advance.
>
>
>
>
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